4XSZ

Crystal structure of CBR 9393 bound to Escherichia coli RNA polymerase holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.

Bae, B.Nayak, D.Ray, A.Mustaev, A.Landick, R.Darst, S.A.

(2015) Proc Natl Acad Sci U S A 112: E4178-E4187

  • DOI: 10.1073/pnas.1502368112
  • Primary Citation of Related Structures:  
    4XSX, 4XSY, 4XSZ

  • PubMed Abstract: 
  • RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center ...

    RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg(2+) ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. We report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.


    Organizational Affiliation

    The Rockefeller University, New York, NY 10065; darst@rockefeller.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABGH239Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoAEcE24377A_3778
EC: 2.7.7.6
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Go to UniProtKB:  A7ZSI4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCI1342Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoBEcE24377A_4528
EC: 2.7.7.6
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Go to UniProtKB:  A7ZUK1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'DJ1407Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoCEcE24377A_4529
EC: 2.7.7.6
Find proteins for A7ZUK2 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaEK91Escherichia coli ATCC 8739Mutation(s): 0 
Gene Names: rpoZEcolC_0062
EC: 2.7.7.6
Find proteins for B1IYV1 (Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDFL522Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42U
Query on 42U

Download Ideal Coordinates CCD File 
C, I
4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline
C22 H23 F4 N5
OXSJLZKYOPQBJE-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.444α = 90
b = 206.331β = 90
c = 309.607γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-01-22 
  • Released Date: 2015-07-22 
  • Deposition Author(s): Bae, B., Darst, S.A.

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description